John Lepyon enlisted with Company F of the 29th Colored Connecticut Infantry Regiment on December 2, 1863. He was appointed First Sergeant on January 1, 1864. Lepyon returned to Cornwall for a week in February 1864 to recover from an illness. On May 1, 1865, Lepyon was demoted to Duty Sergeant. He mustered out at Brownsville, Texas on October 24, 1865.
After the war, Lepyon moved to Canaan, where he married Frances “Fannie” Ten Eyck and found work as a stationery engineer and laborer for the railroad. The couple had two daughters, Clara and Marcella.